First, the nice thing. About half-way through his comments Professor Coyne writes:

My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these--Rich Lenski's study-- extends over several decades).

Thanks. Much appreciated.

Next, he turns to damage control. Directly after the mild compliment, Coyne registers his main complaint about the paper: the conclusions supposedly can only be applied to laboratory evolution experiments and say little about (Darwinian) evolution in nature. "But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons." Below I deal with Coyne's three reasons in turn.

Professor Coyne's first objection is:

1. In virtually none of the experiments summarized by Behe was there the possibility of adapting the way that many bacteria and viruses actually adapt in nature: by the uptake of DNA from other microbes. Lenski's studies of E. coli, for instance, and Bull's work on phage evolution, deliberately preclude the presence of other species that could serve as vectors of DNA, and thus of new FCTs.

Coyne is simply wrong here, at least about phages (bacterial viruses). Viruses grow in other organisms -- the cells they infect. Thus pretty much by definition they are in contact with other microbes for much of their life cycle, and it is thought that sometimes viruses acquire genes from their host cells. In fact, in one report by Bull's group I reviewed, in which the gene for bacteriophage T7 ligase was intentionally removed at the start of an experiment, the investigators reported they initially expected the missing gene to be replaced.

At the outset, our expectation from work in other viral systems was that the loss of ligase activity would remain so deleterious to T7 that recovery to high fitness would require the genome to acquire new sequences through recombination or gene duplication and to replace ligase function by divergence of those sequences.

Unexpectedly, however, "This hope was not realized, and compensatory evolution occurred through point mutations and a deletion." Thus it seems that Professor Coyne's expectations about what is required for a gain-of-FCT event are not universally shared among scientists.

Coyne is of course correct that in experiments in which just one species of bacteria is present, the cells cannot acquire DNA from other species of bacteria. Yet those who conducted such experiments often had expectations for evolution much different from him. In the 1970s and 1980s many workers thought that gene duplication or recruitment plus divergence would allow bacteria to diversify the foodstuffs they could metabolize. Out of many such experiments, only one seemed to work by gain-of-FCT. Professor Coyne's dismissal of such experiments is pure hindsight.

Professor Coyne doesn't mention that in the review I argue that results from nature are consonant with conclusions drawn from lab experiments. I wrote:

One objection might be that the above examples are artificial. They concern laboratory evolution.... Nonetheless, results arguably similar to those that have been seen in laboratory evolution studies to date have also been seen in nature, such as the loss of many genes by Yersinia pestis (after, of course, the acquisition of new genetic material in the form of several plasmids), and the loss-of-FCT mutations that have spread in human populations in response to selective pressure from malaria. A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Coyne's second objection is the following:

2. In relatively short-term lab experiments there has simply not been enough time to observe the accumulation of complex FCTs, which take time to build or acquire from a rare horizontal transmission event.

I addressed that very point in my review:

Furthermore, although complex gain-of-FCT mutations likely would occur only on long time-scales unavailable to laboratory studies, simple gain-of-FCT mutations need not take nearly as long. As seen in Table 1, a gain-of-FCT mutation in sickle hemoglobin is triggered by a simple point mutation, which helps code for a new protein binding site. It has been estimated that new transcription-factor binding sites in higher eukaryotes can be formed relatively quickly by single point mutations in DNA sequences that are already near matches (Stone and Wray 2001). In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand- to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of-FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

Yes, complex gain-of-FCT events would not be expected to occur, but simple GOF's would. Yet they didn't show up.

Professor Coyne then proceeds to put words in my mouth:

What [Be]he's saying is this: "Yes, gain of FCTs could, and likely is, more important in nature than seen in these short-term experiments. But my conclusions are limited to these types of short-term lab studies."

Above I quoted Coyne talking about "complex FCTs, which take time to build or acquire from a rare horizontal transmission event." Yet cells aren't going to sit around twiddling their thumbs until that rare event shows up. Any mutation which confers an advantage at any time will be selected, and the large majority of those in the short term will be LOF. Ironically, Coyne seems to underestimate the power of natural selection, which "is daily and hourly scrutinising, throughout the world, every variation, even the slightest...." A process which scrutinizes life "daily and hourly," as Darwin wrote, isn't going to wait around for some rare event.

Professor Coyne's third objection is:

3. Finally, Behe does not mention--and I think he should have--the extensive and very strong evidence for adaptation via gain-of-FCT mutations in eukaryotes.

As I show in Table 1 of the review, we have wonderful evidence of what Darwinian evolution has done to a multicellular eukaryotic species -- Homo sapiens -- in response to strong selective pressure from malaria over the past ten thousand years. A handful of mutations have been selected. The mutations are classified as: one GOF (the sickle mutation); two modification of functions; and five LOFs. That's pretty much the proportion of what one sees in bacteria and larger viruses, so there is no reason to think that short-term evolution in eukaryotes has a substantially different spectrum of adaptive mutations than for prokaryotes.

Coyne wants to focus on long-term evolution:

While [eukaryotes] may occasionally acquire genes or genetic elements by horizontal transfer, we know that they acquire new genes by the mechanism of gene duplication and divergence: new genes arise by duplication of old ones, and then the functions of these once-identical genes diverge as they acquire new mutations. ... Think of all the genes that have arisen in eukaryotes in this way and gained novel function: classic examples include genes of the immune system, Hox gene families, olfactory genes, and the globin genes.

Unfortunately, Professor Coyne isn't making a critical distinction here. While we may know (or at least have very good evidence that is consonant with the idea) that new genes have arisen by duplication and divergence of old ones in eukaryotes, we do not know that happens by a Darwinian mechanism of random mutation and natural selection. And if some duplicate genes do arise and diversify by Darwinian processes, we do not know that explains all or even most of them. After all, while the long-term processes that Professor Coyne envisions are taking their sweet time to come together, the fast and dirty short-term adaptive processes will dominate. That's what we know from the great efforts put into experimental evolutionary studies by many investigators over decades.

And as I point out in the QRB paper, all of this can be neatly summarized by The First Rule of Adaptive Evolution: Break or blunt any functional coded element whose loss would yield a net fitness gain.